Raw content of Bio::EnsEMBL::Utils::Converter
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=head1 AUTHOR
Juguang Xiao <juguang@tll.org.sg>
=cut
=head1 NAME
Bio::EnsEMBL::Utils::Converter, a converter factory
=head1 SYNOPSIS
my $converter = Bio::EnsEMBL::Utils::Converter->new(
-in => 'Bio::SeqFeature::Generic',
-out => 'Bio::EnsEMBL::SimpleFeature'
);
my ( $fearture1, $feature2 );
my $ens_simple_features =
$converter->convert( [ $feature1, $feature2 ] );
my @ens_simple_features = @{$ens_simple_features};
=head1 DESCRIPTION
Module to converter the business objects between EnsEMBL and any other
projects, currently BioPerl.
What the ready conversions are,
Bio::SeqFeature::Generic <-> Bio::EnsEMBL::SeqFeature, Bio::EnsEMBL::SimpleFeature
Bio::SeqFeature::FeaturePair <-> Bio::EnsEMBL::SeqFeature, Bio::EnsEMBL::RepeatFeature
Bio::Search::HSP::GenericHSP -> Bio::EnsEMBL::BaseAlignFeature's submodules
Bio::Tools::Prediction::Gene -> Bio::EnsEMBL::PredictionTranscript
Bio::Tools::Prediction::Exon -> Bio::EnsEMBL::Exon
Bio::Pipeline::Analysis -> Bio::EnsEMBL::Analysis
=head1 METHODS
=cut
package Bio::EnsEMBL::Utils::Converter;
use strict;
use Bio::EnsEMBL::Root;
our @ISA =qw(Bio::EnsEMBL::Root);
=head2 new
Title : new
Usage :
my $converter = Bio::EnsEMBL::Utils::Converter->new(
-in => 'Bio::SeqFeature::Generic',
-out => 'Bio::EnsEMBL::SimpleFeature'
);
Function: constructor for converter object
Returns : L<Bio::EnsEMBL::Utils::Converter>
Args :
in - the module name of the input.
out - the module name of the output.
analysis - a Bio::EnsEMBL::Analysis object, if converting other objects to EnsEMBL features.
contig - a Bio::EnsEMBL::RawContig object, if converting other objects to EnsEMBL features.
=cut
sub new {
my ($caller, @args) = @_;
my $class = ref($caller) || $caller;
if($class =~ /Bio::EnsEMBL::Utils::Converter::(\S+)/){
my $self = $class->SUPER::new(@args);
$self->_initialize(@args);
return $self;
}else{
my %params = @args;
@params{map {lc $_} keys %params} = values %params;
my $module = $class->_guess_module($params{-in}, $params{-out});
return undef unless($class->_load_module($module));
return "$module"->new(@args);
}
}
# This would be invoked by sub-module's _initialize.
sub _initialize {
my ($self, @args) = @_;
my ($in, $out) = $self->_rearrange([qw(IN OUT)], @args);
$self->in($in);
$self->out($out);
}
=head2 _guess_module
Usage : $module = $class->_guess_module(
'Bio::EnsEMBL::SimpleFeature',
'Bio::EnsEMBL::Generic'
);
=cut
sub _guess_module {
my ($self, $in, $out) = @_;
if($in =~ /^Bio::EnsEMBL::(\S+)/ and $out =~ /^Bio::EnsEMBL::(\S+)/){
$self->throw("Cannot convert between EnsEMBL objects.\n[$in] to [$out]");
}elsif($in =~ /^Bio::EnsEMBL::(\S+)/){
return 'Bio::EnsEMBL::Utils::Converter::ens_bio';
}elsif($out =~ /^Bio::EnsEMBL::(\S+)/){
return 'Bio::EnsEMBL::Utils::Converter::bio_ens';
}else{
$self->throw("Cannot convert between non-EnsEMBL objects.\n[$in] to [$out]");
}
}
=head2 convert
Title : convert
Usage : my $array_ref = $converter->convert(\@input);
Function: does the actual conversion
Returns : an array ref of converted objects
Args : an array ref of converting objects
=cut
sub convert{
my ($self, $input) = @_;
$input || $self->throw("Need a ref of array of input objects to convert");
my $output_module = $self->out;
$self->throw("Cannot load [$output_module] perl module")
unless $self->_load_module($output_module);
unless(ref($input) eq 'ARRAY'){
$self->warn("The input is supposed to be an array ref");
return $self->_convert_single($input);
}
my @output = ();
foreach(@{$input}){
push(@output, $self->_convert_single($_));
}
return \@output;
}
sub _convert_single{
shift->throw("Not implemented. Please check the instance subclass");
}
=head2 in
Title : in
Useage : $self->in
Function : get and set for in
Return :
Args :
=head2 out
Title : out
Useage : $self->out
Function : get and set for out
Return :
Args :
=cut
foreach my $field (qw(in out)){
my $slot=__PACKAGE__ ."::$field";
no strict 'refs';
*$field=sub{
my $self=shift;
$self->{$slot}=shift if @_;
return $self->{$slot};
};
}
=head2 _load_module
This method is copied from Bio::Root::Root
=cut
sub _load_module {
my ($self, $name) = @_;
my ($module, $load, $m);
$module = "_<$name.pm";
return 1 if $main::{$module};
# untaint operation for safe web-based running (modified after a fix
# a fix by Lincoln) HL
if ($name !~ /^([\w:]+)$/) {
$self->throw("$name is an illegal perl package name");
}
$load = "$name.pm";
my $io = Bio::Root::IO->new();
# catfile comes from IO
$load = $io->catfile((split(/::/,$load)));
eval {
require $load;
};
if ( $@ ) {
$self->throw("Failed to load module $name. ".$@);
}
return 1;
}
1;
]]>